Differences

This shows you the differences between two versions of the page.

Link to this comparison view

start [2013/12/20 13:15]
igor
start [2014/09/25 13:10] (current)
igor
Line 1: Line 1:
-====== Welcome to BacTrack ​Wiki pages ======+====== Welcome to BactImAs ​Wiki pages ======
  
  
-BacTrack ​is an open-source multi platform java application intended to assist the researcher in tracking various organisms in sequences of images and obtaining and visualizing their quantitative data.  ​+**BactImAs ​is an open-source multi platform java application** intended to assist the researcher in tracking various organisms in sequences of images and obtaining and visualizing their quantitative data.  ​
  
 +Bactimas paper is published here: [[http://​dx.doi.org/​10.1186/​1471-2105-15-251|DOI:​10.1186/​1471-2105-15-251]]
  
-Motivation:+ 
 + 
 +**Motivation:**
 A common task in today’s synthetic and systems biology studies is the analysis of various features of organisms using movies obtained through time-lapse microscopy. \\ A common task in today’s synthetic and systems biology studies is the analysis of various features of organisms using movies obtained through time-lapse microscopy. \\
 This process consists of identifying organisms on a large number of images and measuring their features whilst keeping track of their lineage which is **a very cumbersome and error prone task** for the researcher. \\  This process consists of identifying organisms on a large number of images and measuring their features whilst keeping track of their lineage which is **a very cumbersome and error prone task** for the researcher. \\ 
 To facilitate the analysis, various mostly automated tools and algorithms were developed in recent years but all of them targeting rather specific organisms and/or laboratory setups, since a general purpose automated solution to this detection problem is extremely hard if not impossible. \\ To facilitate the analysis, various mostly automated tools and algorithms were developed in recent years but all of them targeting rather specific organisms and/or laboratory setups, since a general purpose automated solution to this detection problem is extremely hard if not impossible. \\
  
-Solution: +**Solution:** 
-We've designed ​bactrack ​as a "​platform",​ that is as a collection of somewhat independent well defined modules working together. Such setup facilitates maintenance,​ customization and upgrades. +We've designed ​BactImAs ​as a "​platform",​ that is as a collection of somewhat independent well defined modules working together. Such setup facilitates maintenance,​ customization and upgrades. 
-This property is particularly useful for the tracking algorithms - in BacTrack ​it is possible to include **multiple tracking algorithms** ("​best-of-breed approach"​) and thus use the best fitted algoritm for the problem at hand.  \\ +This property is particularly useful for the tracking algorithms - in BactImAs ​it is possible to include **multiple tracking algorithms** ("​best-of-breed approach"​) and thus use the best fitted algoritm for the problem at hand.  \\ 
-It is even possible to mix-and-match algorithms in a way to  ​+It is even possible to mix-and-match algorithms in a way to segment one part of the movie with algorithm A and the other part with algorithm B. 
 +  
 + 
 +BactImAs uses a semi-automated approach: it relies on the user to define the initial cells and all cell divisions. Other than that, the application tracks cells using a our newly developed algorithm. At any point, the user can intervene and correct any unsatisfactory cell detections. 
 + 
 +BactImAs provides the following features: 
 + 
 +  * Easy to use GUI interface  
 +  * Frame anlignment algorithm  
 +  * Novel mycobacteria segmentation algorithm 
 +  * Novel configurable lineage tree visualization 
 +  * Automated acquisition of quantitative date 
 +  * Relational database storage, SQL interface to data 
 +  * Data export (CSV) 
  
-BacTrack uses a semi-automated approach: it relies on the researcher to define the initial cells and all cell divisions. Other than that, the application tracks cells using a newly developed algorithm described here. At any point, a researcher can intervene and correct any unsatisfactory cell detections. We’ve tested on four different organisms and obtained promising results. The application enables configurable lineage tree visualization and data export for use in third party programs.  ​+----
  
  
 +{{:​bactrack_main.png?​400|}}
 +{{:​btree.png?​400|}}
 +{{:​frame.png?​400|}}
 +{{:​segmentation.png?​400|}}
  
-Unlike most approaches (REFS here), our aim is to build a general-purpose solution for tracking and analysis of various organisms. To that end, it is necessary to build a multi-platform,​ user-friendly application that is open to changes and additions. Furthermore,​ we believe it is important to enable ways for researchers to collaborate and easily exchange their analysis, so that they can reproduce other’s results and/or take on a different perspective on existing, already processed data (movies). With that in mind, we’ve designed the application to be in some ways similar to movie editing software (e.g. LightWorks, Pinnacle Studio, etc.) where the user is given full command of every step of the detection process (Fig 1). User can set or modify selections at any frame. For this purpose application leverages the ImageJ program - an excellent open-source program well known to the biology community and heavily used in image processing and analysis. But unlike others, we’ve taken the source code of ImageJ and incorporated it into our project, so that we can retain full control of our graphical user interface and program behaviourbehavior. ​ 
-{{:​bactrack_main.png?​200|}} 
-{{:​btree.png?​200|}} 
-{{:​frame.png?​200|}} 
-{{:​segmentation.png?​200|}} 
  
  
Line 29: Line 45:
  
  
 +----
 +Example reports produced by BactImAs:
  
-{{youtube>​xSpLbs5pe_Y?​large|Report video generated from the program }}+{{youtube>​xSpLbs5pe_Y?​medium|BW Report video generated from the program ​(black outline - computer, white - human) }}  
 +{{youtube>​GKMdunbu6CM?​medium|Color report video generated from the program (green outline - human, red - human) ​}}
Print/export
QR Code
QR Code start (generated for current page)